Contacts of the helix formed by residues 82 - 112 (chain P) in PDB entry 3IS7
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 82 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143N LYS* 6.6 0.2 - - - -
35P TRP* 4.0 9.6 - - + -
81P GLU* 1.3 80.2 - - - +
83P THR* 1.3 66.7 + - - +
84P GLN* 3.3 8.1 + - - +
85P GLU* 3.1 36.2 + - - +
86P MET* 2.8 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 83 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32P TRP* 2.9 38.1 + - + +
35P TRP* 4.4 3.8 - - - -
37P LEU* 3.9 5.2 - - - +
40P LEU* 4.0 12.8 - - + -
82P ASN* 1.3 76.2 - - - +
84P GLN* 1.3 64.5 + - - +
86P MET* 3.2 4.4 + - - +
87P LEU* 3.0 40.2 + - + +
141P ILE* 4.9 2.0 - - + -
146P LEU* 5.3 3.4 - - - -
149P TYR* 4.4 5.4 - - + -
150P LEU* 3.5 28.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 84 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82P ASN* 3.3 7.6 + - - +
83P THR* 1.3 78.7 - - - +
85P GLU* 1.3 57.5 + - + +
87P LEU* 3.5 11.4 + - - +
88P GLN* 2.9 29.6 + - + +
138P LEU* 3.7 26.7 + - + +
141P ILE* 4.0 29.0 - - + +
142P GLN* 4.2 19.7 + - - +
146P LEU* 5.2 12.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 85 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79P ILE 5.0 0.2 - - - +
80P GLY* 3.6 6.2 - - - -
81P GLU* 2.7 49.1 + - - +
82P ASN* 3.1 28.6 + - - +
84P GLN* 1.3 74.8 - - + +
86P MET* 1.3 61.6 + - - +
88P GLN* 3.2 5.6 + - - +
89P CYS* 2.8 35.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 86 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28P HIS* 3.6 58.6 - - + +
31P MET* 4.0 17.5 - - + -
32P TRP* 3.6 34.3 - - + +
35P TRP* 3.4 29.2 - - + -
80P GLY* 3.6 13.0 - - - -
82P ASN* 2.8 24.9 + - - +
83P THR 3.5 3.6 - - - +
85P GLU* 1.3 75.9 - - - +
87P LEU* 1.3 64.6 + - - +
89P CYS* 3.2 3.8 + - - +
90P ASP* 3.0 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32P TRP* 4.1 17.0 - - + -
40P LEU* 4.7 7.2 - - + -
44P GLU* 5.9 0.4 - - - +
83P THR* 3.0 31.4 + - + +
84P GLN 3.8 2.7 - - - +
86P MET* 1.3 76.8 - - - +
88P GLN* 1.3 56.7 + - - +
90P ASP* 3.2 5.6 + - - +
91P LEU* 2.9 27.9 + - - +
133P TYR* 4.7 3.6 - - + -
134P LEU* 3.9 28.4 - - + +
137P GLN* 4.1 26.7 - - + -
138P LEU* 3.8 19.9 - - + +
141P ILE* 3.8 28.9 - - + -
149P TYR* 4.3 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 88 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84P GLN* 2.9 20.3 + - + +
85P GLU* 3.2 6.7 + - - +
87P LEU* 1.3 76.1 - - - +
89P CYS* 1.3 53.2 + - - +
91P LEU* 3.1 22.1 + - - +
92P ASN* 2.7 72.3 + - - +
95P LEU* 5.6 1.0 - - - +
138P LEU* 3.9 20.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 89 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24P GLN* 3.3 10.0 + - - +
28P HIS* 4.1 2.7 - - + -
78P LEU* 3.4 44.0 - - + +
79P ILE 4.1 2.2 - - - -
80P GLY* 4.0 15.0 - - - -
85P GLU* 2.8 24.3 + - - +
86P MET 3.3 7.2 - - - +
88P GLN* 1.3 78.0 - - - +
90P ASP* 1.3 55.7 + - - +
92P ASN* 3.5 9.5 + - - +
93P LEU* 2.9 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 90 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24P GLN* 3.0 16.4 + - - +
25P TYR* 3.5 17.8 + - + -
28P HIS* 2.8 24.7 + - - -
32P TRP* 4.6 5.2 - - - -
44P GLU* 2.2 34.0 - - - +
86P MET 3.0 14.0 + - - +
87P LEU* 3.5 8.2 - - - +
89P CYS* 1.3 75.8 - - - +
91P LEU* 1.3 58.3 + - - +
93P LEU* 3.3 2.6 + - - +
94P GLU* 3.0 31.7 + - - +
130P HIS* 4.5 1.3 - - + -
134P LEU* 4.0 22.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 91 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87P LEU 2.9 13.9 + - - +
88P GLN* 3.1 24.9 + - - +
90P ASP* 1.3 74.5 - - - +
92P ASN* 1.3 65.7 + - - +
94P GLU* 3.1 2.4 + - - -
95P LEU* 2.9 48.8 + - + +
131P ILE* 3.9 32.8 - - + -
134P LEU* 4.0 16.5 - - + +
135P GLU* 4.2 24.9 - - + +
138P LEU* 4.0 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 92 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78P LEU* 4.2 13.0 - - + +
88P GLN* 2.7 54.7 + - - +
89P CYS* 3.7 10.9 - - - +
91P LEU* 1.3 71.7 - - - +
93P LEU* 1.3 63.5 + - - +
95P LEU* 3.4 12.1 + - - +
96P LYS* 3.2 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 93 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17P ASN* 5.3 7.4 - - + +
20P ILE* 3.8 25.4 - - + -
21P ALA* 3.6 41.7 - - + +
24P GLN* 3.7 22.9 - - - +
25P TYR* 4.0 7.4 - - + +
76P LYS 5.1 2.0 - - - +
78P LEU* 4.1 16.3 - - + +
89P CYS 2.9 18.2 + - - +
90P ASP 3.7 3.6 - - - +
91P LEU 3.1 0.2 - - - -
92P ASN* 1.3 79.1 - - - +
94P GLU* 1.3 62.6 + - - +
96P LYS* 3.4 14.3 + - + +
97P ALA* 3.1 21.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 94 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21P ALA* 5.8 0.4 - - - -
25P TYR* 2.6 31.2 + - - +
51P GLU* 3.6 3.6 - - - +
90P ASP 3.0 17.1 + - - +
91P LEU* 3.1 4.2 + - - +
93P LEU* 1.3 74.4 - - - +
95P LEU* 1.3 65.1 + - - +
97P ALA* 3.1 8.1 + - - +
98P THR* 3.0 27.5 + - - -
127P GLU* 2.3 46.0 - - - +
130P HIS* 3.1 27.8 + - + +
131P ILE* 3.6 23.1 - - + -
134P LEU* 4.4 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 95 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88P GLN* 5.6 0.9 - - - +
91P LEU* 2.9 43.9 + - + +
92P ASN* 3.7 12.6 - - - +
93P LEU 3.3 0.2 - - - -
94P GLU* 1.3 74.7 - - - +
96P LYS* 1.3 63.7 + - - +
98P THR* 3.5 10.6 + - + +
99P LYS* 3.3 20.1 + - - +
131P ILE* 4.2 20.4 - - + -
135P GLU* 6.0 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 96 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13P LYS* 4.1 14.5 - - - +
17P ASN* 4.4 14.0 + - - +
92P ASN 3.2 10.9 + - - +
93P LEU* 3.7 16.8 - - + +
94P GLU 3.2 0.6 - - - -
95P LEU* 1.3 81.5 - - - +
97P ALA* 1.3 63.3 + - - +
99P LYS* 3.4 15.2 + - - +
100P ASP* 2.6 48.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 97 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14P ILE* 5.1 0.7 - - - +
17P ASN* 4.1 26.7 + - + +
18P GLU* 6.0 1.8 - - - +
51P GLU* 6.2 0.2 - - - +
93P LEU* 3.1 15.5 + - + +
94P GLU* 3.1 21.8 + - - +
96P LYS* 1.3 77.3 - - - +
98P THR* 1.3 58.1 + - - +
100P ASP* 3.3 4.9 + - - +
101P LEU* 2.9 39.6 + - + +
127P GLU* 5.0 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 98 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94P GLU 3.0 14.6 + - - -
95P LEU* 3.7 12.3 - - + +
97P ALA* 1.3 75.7 - - - +
99P LYS* 1.3 62.3 + - + +
101P LEU* 3.2 9.2 + - - +
102P ARG* 2.9 58.7 + - - +
124P LEU* 3.3 17.7 - - - +
127P GLU* 4.1 10.0 - - - +
128P GLU* 4.4 2.3 - - - +
131P ILE* 4.0 18.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 99 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95P LEU 3.3 9.9 + - - +
96P LYS* 3.4 17.4 + - - +
98P THR* 1.3 81.1 - - - +
100P ASP* 1.3 69.3 + - - +
102P ARG* 3.2 10.6 + - - +
103P GLU* 3.1 46.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 100 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10P HIS* 5.0 1.7 + - - -
13P LYS* 3.7 22.3 + - + -
14P ILE* 3.7 16.4 - - + +
17P ASN* 2.9 26.6 + - - +
96P LYS* 2.6 46.0 + - - +
97P ALA 3.5 7.9 - - - +
99P LYS* 1.3 82.4 + - - +
101P LEU* 1.3 61.8 + - - +
103P GLU* 3.3 19.4 + - - +
104P ALA* 3.2 17.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14P ILE* 3.3 34.9 - - + +
18P GLU* 5.3 0.9 - - - +
97P ALA* 2.9 28.3 + - + +
98P THR* 3.2 8.7 + - - +
100P ASP* 1.3 76.1 - - - +
102P ARG* 1.3 64.0 + - - +
104P ALA* 3.2 2.7 + - - +
105P ILE* 3.1 28.8 + - + +
120P LEU* 3.6 35.7 - - + +
123P ILE* 3.9 23.6 - - + -
124P LEU* 4.1 17.9 - - + -
127P GLU* 4.0 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 102 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98P THR* 2.9 41.6 + - - +
99P LYS* 3.7 8.0 - - - +
100P ASP 3.2 0.6 - - - -
101P LEU* 1.3 76.4 - - - +
103P GLU* 1.3 62.5 + - + +
105P ILE* 3.2 4.2 + - - +
106P VAL* 3.1 27.7 + - - +
124P LEU* 3.8 20.3 - - + +
128P GLU* 2.7 31.6 + - - -
111Q VAL 5.4 0.7 - - - -
112Q HIS* 2.7 51.0 + - + +
113Q ASP* 4.0 9.1 + - - +
114Q TYR* 4.0 14.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 103 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10P HIS* 3.9 16.4 - - + -
13P LYS* 5.2 4.7 + - - -
99P LYS* 3.1 42.7 + - + +
100P ASP* 3.4 22.9 - - - +
101P LEU 3.2 0.2 - - - -
102P ARG* 1.3 78.7 - - + +
104P ALA* 1.3 62.7 + - - +
106P VAL* 3.4 9.0 + - - +
107P HIS* 3.2 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 104 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10P HIS* 3.7 33.8 + - + +
14P ILE* 4.2 11.9 - - + -
100P ASP 3.2 15.8 + - - +
101P LEU 3.8 2.9 - - - +
102P ARG 3.2 0.2 - - - -
103P GLU* 1.3 80.0 - - - +
105P ILE* 1.3 57.5 + - - +
107P HIS* 3.3 2.9 + - - +
108P CYS* 3.0 30.8 + - - -
120P LEU* 3.7 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 105 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101P LEU 3.1 20.0 + - - +
102P ARG 3.7 5.8 - - - +
104P ALA* 1.3 75.8 - - - +
106P VAL* 1.3 65.8 + - - +
108P CYS* 3.3 6.9 + - - +
109P GLU* 3.0 22.5 + - - +
117P ARG* 3.8 29.8 - - + +
120P LEU* 3.8 24.2 - - + +
121P LYS* 4.1 24.5 - - + +
124P LEU* 4.2 13.0 - - + -
114Q TYR* 3.4 47.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 106 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102P ARG 3.1 14.8 + - - +
103P GLU* 3.6 9.6 - - - +
105P ILE* 1.3 78.8 - - - +
107P HIS* 1.3 64.9 + - + +
109P GLU* 3.4 5.5 + - - +
110P GLN* 3.1 30.5 + - + +
112Q HIS* 3.7 28.9 - - + +
114Q TYR* 3.2 21.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 107 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4P ASP* 2.8 29.0 + - - -
6P LYS* 3.2 33.5 - - + +
7P VAL* 3.7 17.0 - - + -
10P HIS* 3.7 27.2 + + + +
103P GLU 3.2 4.8 + - - +
104P ALA 3.7 6.7 - - - +
105P ILE 3.1 0.4 - - - -
106P VAL* 1.3 78.8 - - + +
108P CYS* 1.3 60.7 + - - +
110P GLN* 3.1 27.4 + - - +
111P VAL* 2.9 43.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 108 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7P VAL* 4.2 20.2 - - - -
10P HIS* 6.0 1.8 - - - -
11P LEU* 5.4 0.4 - - - -
104P ALA* 3.0 20.7 + - - +
105P ILE 3.3 5.1 + - - +
107P HIS* 1.3 76.7 - - - +
109P GLU* 1.3 51.7 + - - +
111P VAL* 3.2 8.9 + - - -
112P HIS 2.7 31.2 + - - -
113P ASP* 2.9 26.5 + - - +
116P SER* 3.6 28.0 - - - -
117P ARG* 4.0 10.8 - - + -
120P LEU* 3.9 15.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 109 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109I GLU* 4.1 10.2 - - - +
117I ARG* 2.5 32.7 + - - -
105P ILE 3.0 13.8 + - - +
106P VAL* 3.5 10.1 - - - +
108P CYS* 1.3 74.0 - - - +
110P GLN* 1.3 60.8 + - - +
112P HIS* 2.9 29.0 + - - +
114P TYR* 3.6 17.5 + - - -
117P ARG* 3.0 40.0 + - - +
109Q GLU* 4.2 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 110 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106P VAL* 3.1 21.1 + - + +
107P HIS* 3.1 30.1 + - - +
109P GLU* 1.3 82.6 - - - +
111P VAL* 1.3 67.8 + - + +
112P HIS* 3.7 11.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 111 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102I ARG* 5.4 0.5 - - - -
4P ASP* 3.8 27.4 - - + +
7P VAL* 3.7 29.6 - - + -
107P HIS* 2.9 34.0 + - + +
108P CYS 3.9 4.5 - - - +
110P GLN* 1.3 82.0 - - + +
112P HIS* 1.3 72.2 + - - +
113P ASP* 3.4 7.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 112 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102I ARG* 3.0 36.6 + - + +
106I VAL* 3.7 25.8 - - + +
108P CYS 2.7 12.8 + - - -
109P GLU 2.9 19.5 + - - -
110P GLN 3.7 9.9 + - - -
111P VAL* 1.3 75.8 + - - +
113P ASP* 1.3 57.4 + - - +
114P TYR* 3.1 44.5 + + + +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il